Issue with compiling mpi4py and python 3.9 on centOS

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mani raman

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Nov 22, 2022, 9:21:55 AM11/22/22

to mpi4py

Hello,

I am trying to build mpi4py with python 3.9 on our slurm cluster (with out sudo rights).

There is an error popping up as follows. Any suggestion will be helpful.

Collecting mpi4py

Using cached mpi4py-3.1.4.tar.gz (2.5 MB)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Building wheels for collected packages: mpi4py

Building wheel for mpi4py (pyproject.toml) ... error

error: subprocess-exited-with-error

× Building wheel for mpi4py (pyproject.toml) did not run successfully.

│ exit code: 1

╰─> [165 lines of output]

running bdist_wheel

running build

running build_src

running build_py

creating build

creating build/lib.linux-x86_64-cpython-39

creating build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/__main__.py -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/bench.py -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/run.py -> build/lib.linux-x86_64-cpython-39/mpi4py

creating build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/__main__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/_base.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/_core.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/_lib.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/aplus.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/pool.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/server.py -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

creating build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/util/__init__.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/util/dtlib.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/util/pkl5.py -> build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/py.typed -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/MPI.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/__main__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/bench.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/dl.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/run.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/MPI.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/__init__.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py

copying src/mpi4py/libmpi.pxd -> build/lib.linux-x86_64-cpython-39/mpi4py

creating build/lib.linux-x86_64-cpython-39/mpi4py/include

creating build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/include/mpi4py/mpi4py.h -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/include/mpi4py/mpi4py.i -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/include/mpi4py/mpi.pxi -> build/lib.linux-x86_64-cpython-39/mpi4py/include/mpi4py

copying src/mpi4py/futures/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/__main__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/_core.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/_lib.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/aplus.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/pool.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/futures/server.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/futures

copying src/mpi4py/util/__init__.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/util/dtlib.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util

copying src/mpi4py/util/pkl5.pyi -> build/lib.linux-x86_64-cpython-39/mpi4py/util

running build_clib

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler: /data/beegfs/home/periyamn/opt/bin/mpicc

checking for library 'lmpe' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -I/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -c _configtest.c -o _configtest.o

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -llmpe -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -llmpe: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

building 'mpe' dylib library

creating build/temp.linux-x86_64-cpython-39

creating build/temp.linux-x86_64-cpython-39/src

creating build/temp.linux-x86_64-cpython-39/src/lib-pmpi

creating build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -shared -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/mpe.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libmpe.so

checking for library 'vt-mpi' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt-mpi -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt-mpi: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for library 'vt.mpi' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt.mpi -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt.mpi: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

building 'vt' dylib library

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -shared -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt.so

checking for library 'vt-mpi' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt-mpi -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt-mpi: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for library 'vt.mpi' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt.mpi -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt.mpi: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

building 'vt-mpi' dylib library

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -shared -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-mpi.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt-mpi.so

checking for library 'vt-hyb' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt-hyb -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt-hyb: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

checking for library 'vt.ompi' ...

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -lvt.ompi -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: cannot find -lvt.ompi: No such file or directory

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

building 'vt-hyb' dylib library

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -shared -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,--no-as-needed build/temp.linux-x86_64-cpython-39/src/lib-pmpi/vt-hyb.o -o build/lib.linux-x86_64-cpython-39/mpi4py/lib-pmpi/libvt-hyb.so

running build_ext

MPI configuration: [mpi] from 'mpi.cfg'

MPI C compiler: /data/beegfs/home/periyamn/opt/bin/mpicc

checking for dlopen() availability ...

checking for header 'dlfcn.h' ...

gcc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -I/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -I/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include/python3.9 -c _configtest.c -o _configtest.o

success!

removing: _configtest.c _configtest.o

success!

checking for library 'dl' ...

gcc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

checking for function 'dlopen' ...

gcc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o _configtest

success!

removing: _configtest.c _configtest.o _configtest

building 'mpi4py.dl' extension

gcc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -I/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -O2 -isystem /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/include/python3.9 -c src/dynload.c -o build/temp.linux-x86_64-cpython-39/src/dynload.o

gcc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat -shared -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -Wl,-rpath-link,/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib -L/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/lib build/temp.linux-x86_64-cpython-39/src/dynload.o -Lbuild/temp.linux-x86_64-cpython-39 -ldl -o build/lib.linux-x86_64-cpython-39/mpi4py/dl.cpython-39-x86_64-linux-gnu.so

checking for MPI compile and link ...

success!

removing: _configtest.c _configtest.o

/data/beegfs/home/periyamn/opt/bin/mpicc -pthread -B /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat _configtest.o -Lbuild/temp.linux-x86_64-cpython-39 -o _configtest

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: warning: libdl.so.2, needed by /data/beegfs/home/periyamn/opt/lib/libmpi.so, not found (try using -rpath or -rpath-link)

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: warning: librt.so.1, needed by /data/beegfs/home/periyamn/opt/lib/libmpi.so, not found (try using -rpath or -rpath-link)

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: warning: libm.so.6, needed by /data/beegfs/home/periyamn/opt/lib/libmpi.so, not found (try using -rpath or -rpath-link)

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: warning: libutil.so.1, needed by /data/beegfs/home/periyamn/opt/lib/libmpi.so, not found (try using -rpath or -rpath-link)

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib/libmpi.so: undefined reference to `ceil@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib//libopen-pal.so.40: undefined reference to `dlopen@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib//libopen-pal.so.40: undefined reference to `dlerror@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib/libmpi.so: undefined reference to `clock_gettime@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib/libmpi.so: undefined reference to `sqrt@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib//libopen-pal.so.40: undefined reference to `openpty@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib//libopen-pal.so.40: undefined reference to `dlclose@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib/libmpi.so: undefined reference to `clock_getres@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib/libmpi.so: undefined reference to `log@GLIBC_2.2.5'

/data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld: /data/beegfs/home/periyamn/opt/lib//libopen-pal.so.40: undefined reference to `dlsym@GLIBC_2.2.5'

collect2: error: ld returned 1 exit status

failure.

removing: _configtest.c _configtest.o

error: Cannot link MPI programs. Check your configuration!!!

[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

ERROR: Failed building wheel for mpi4py

Failed to build mpi4py

ERROR: Could not build wheels for mpi4py, which is required to install pyproject.toml-based projects

Probably the error is with linking the math library. But how do I do it?

Best,

Mani

Lisandro Dalcin

unread,

Nov 22, 2022, 9:46:41 AM11/22/22

to mpi4py

You are trying to install mpi4py within a conda environment. conda-forge uses to install compiler packages, and these interfere with system compilers or in your case with the mpicc compiler wrappers installed outside conda-forge. You can take a look at this old issue https://bitbucket.org/mpi4py/mpi4py/issues/143/ , but I'm not sure the hacks discussed there will help you.

Perhaps you can try uninstalling the compiler packages from the conda environment, or even hack it with "rm /data/beegfs/home/periyamn/miniconda3/envs/dask_mpi/compiler_compat/ld" to remove the "ld" command that is giving you trouble? If you cannot solve your problem, I would suggest contacting the conda-forge folks for advice, perhaps they have a quick an easy way to workaround these issues that I'm not aware of.